It's a personal impression (according to my experience) YRC1000 robots has a different dynamic behavior compared with previous controllers. For example I noticed robot slows down when points are very close to each other (like you are saying) or when you have WAIT IN#(x)=ON instruction even if the input is already ON at execution time, or if you enable PL option in MOV instructions.
I found some improvements upgrading sw to the latest version, so my suggestion is try to upgrade the sw.